mtReadVCF_mtc: mtReadVCF_mtc function

In mtDNA-BU/mtdnaANNO: Annotation of mtDNA sequence variations

mtReadVCF_mtc function

Description

Extract allele, freq and coverage datasets from the VCF file containing results called by mitoCaller. The datasets are the input of mtAAF and mtSummary functions.

Usage

mtReadVCF_mtc(file)

Arguments

file	a string of path and name of VCF file to import

Value

A list contains the three matrices of allele, freq and coverage with dimensions of 16569 x N. Rows correspond to loci and columns correspond to subjects. It contains subject ID as the column names.

Examples

## Not run: 
## Read mitoCaller VCF file
mtVCF_mtc <- mtReadVCF_mtc(file="dir/example.vcf")
allele <- mtVCF_mtc$allele
freq   <- mtVCF_mtc$freq
coverage <- mtVCF_mtc$coverage

## compute AAF
aaf=mtAAF(allele, freq)

## End(Not run)

mtDNA-BU/mtdnaANNO documentation built on Aug. 11, 2022, 10:57 a.m.